diff --git a/NEON-DOMAINS-HSE-2020to2023-edited.csv b/NEON-DOMAINS-HSE-2020to2023-edited.csv
new file mode 100644
index 0000000000000000000000000000000000000000..0c400ec252e229bc358dea4b6caf4898d947e940
--- /dev/null
+++ b/NEON-DOMAINS-HSE-2020to2023-edited.csv
@@ -0,0 +1,20 @@
+domain,alpha,beta,a,b,alpha_R2,alpha_rmse,beta_R2,beta_rmse,HSE,k
+D01,2.1572,0.6012,0.3861,2.4172,0.7948,0.6186,0.6737,0.2475,2.1698,0.1374
+D02,2.271,0.6878,0.3844,1.8789,0.8567,0.6814,0.8163,0.2526,1.6368,0.4157
+D03,2.41,0.5978,0.1554,1.9862,0.7237,1.0622,0.6068,0.3779,1.9355,0.6481
+D04,3.4556,0.3366,0.0487,2.5282,0.553,1.2323,0.3851,0.2721,3.4865,0.0829
+D05,2.4488,0.6189,0.1375,2.3758,0.8349,0.6954,0.7739,0.2372,1.7829,0.4439
+D06,2.8204,0.5321,0.1342,2.0938,0.8734,0.7112,0.6918,0.3004,1.9383,0.4634
+D07,2.3704,0.631,0.2226,2.2403,0.8375,0.75,0.8015,0.2866,1.799,0.3486
+D08,2.6336,0.636,0.1501,2.1019,0.8372,0.8452,0.7857,0.2568,1.5109,0.6445
+D09,,,,,,,,,1.56,
+D10,1.8393,0.5969,0.2969,1.6349,0.5313,0.8107,0.597,0.2815,2.5111,0.6488
+D11,2.9187,0.5095,0.1542,1.6502,0.8263,0.6523,0.6997,0.249,2.0065,0.9081
+D12,2.8231,0.5426,0.0492,1.9606,0.8793,0.7181,0.8643,0.2395,1.8628,1.7008
+D13,2.229,0.7632,0.1119,0.91,0.738,0.7827,0.6317,0.3532,1.3917,11.4434
+D14,,0.8936,,0.5258,,,0.4397,0.2172,1.56,
+D15,2.3559,0.155,0.7807,2.3267,0.4221,0.7376,0.0872,0.2551,11.546,0.0
+D16,2.1004,0.801,0.3335,1.3291,0.8866,0.6551,0.8748,0.2875,1.3965,1.4735
+D17,2.2601,0.7142,0.2322,1.0253,0.754,1.0605,0.813,0.3402,1.5404,4.0151
+D19,2.7256,0.6659,0.0487,1.4185,0.8095,0.7548,0.6888,0.2925,1.2777,7.1902
+D20,2.7748,0.5558,0.0535,2.0948,0.737,1.1261,0.7135,0.3204,1.8238,1.3068
diff --git a/NEON-DOMAINS-HSE-edited.csv b/NEON-DOMAINS-HSE-edited.csv
deleted file mode 100644
index 63b8a4931c2f7e575dc9c2d9ceea2eb0ad54ff57..0000000000000000000000000000000000000000
--- a/NEON-DOMAINS-HSE-edited.csv
+++ /dev/null
@@ -1,20 +0,0 @@
-domain,alpha,beta,a,b,alpha_R2,alpha_pval,beta_R2,beta_pval,HSE
-D01,2.2529,0.6684,0.2941,1.9426,0.8507,0.0,0.8511,0.0,1.7394
-D02,2.2898,0.6779,0.3637,1.9245,0.8637,0.0,0.9117,0.0,1.6605
-D03,2.1601,0.6945,0.2718,1.4214,0.7379,0.0,0.6534,0.0,1.7197
-D04,3.4471,0.3531,0.0488,2.4232,0.5582,0.0,0.5106,0.0,1.63
-D05,2.4682,0.6332,0.1302,2.2676,0.8379,0.0,0.8523,0.0,1.6902
-D06,2.8065,0.5706,0.1382,1.827,0.8751,0.0,0.7824,0.0,1.6987
-D07,2.3715,0.6612,0.2218,2.0167,0.8424,0.0,0.8638,0.0,1.6532
-D08,2.6293,0.6481,0.1524,2.0092,0.8465,0.0,0.8781,0.0,1.4565
-D09,2.6293,0.6481,0.1524,2.0092,0.8465,0.0,0.8781,0.0,1.4
-D10,1.842,0.6368,0.2951,1.4466,0.5332,0.0,0.7382,0.0,1.64
-D11,2.8714,0.5037,0.1665,1.6619,0.8479,0.0,0.8002,0.0,2.0995
-D12,2.8057,0.5405,0.0509,1.9685,0.8805,0.0,0.8839,0.0,1.8946
-D13,2.2293,0.7366,0.1107,0.9696,0.7682,0.0,0.7332,0.0,1.4859
-D14,2.2293,0.7366,0.1107,0.9696,0.7682,0.0,0.7332,0.0,1.63
-D15,2.6712,0.2131,0.4856,1.9758,0.4674,0.0,0.2408,0.0,1.4
-D16,2.1532,0.7264,0.2881,1.6187,0.8899,0.0,0.8753,0.0,1.6
-D17,2.2558,0.6884,0.2354,1.0662,0.7653,0.0,0.8462,0.0,1.6495
-D19,2.6941,0.6635,0.0513,1.3985,0.8359,0.0,0.7813,0.0,1.3201
-D20,2.7748,0.559,0.0535,2.0775,0.737,0.0,0.7569,0.0,1.8029
diff --git a/arojas_biomass_gedi.yml b/arojas_biomass_gedi.yml
deleted file mode 100644
index 16c72dc3cffdea79f4326ccf407011b0453884ae..0000000000000000000000000000000000000000
--- a/arojas_biomass_gedi.yml
+++ /dev/null
@@ -1,21 +0,0 @@
-algorithm_description: Estimate biomass using GEDI data
-algorithm_name: arojas_biomass_gedi
-algorithm_version: master
-build_command: biomass-gedi-conus/build-env.sh
-disk_space: 8gbGB
-docker_container_url: mas.maap-project.org/root/maap-workspaces/base_images/vanilla:v3.0.1
-inputs:
- config: []
- file: []
- positional:
- - default: ''
- description: ''
- name: L1B_URL
- required: false
- - default: ''
- description: ''
- name: L2A_URL
- required: false
-queue: maap-dps-worker-16gb
-repository_url: https://repo.maap-project.org/arojearthdata/biomass-gedi-conus.git
-run_command: biomass-gedi-conus/run.sh
diff --git a/main.py b/main.py
index 4e773a327b8273cd58c9229a06417e8d693ea1cc..fd9ae0d9fe7348e0f6b6735ad3c5aa3ad9d1b606 100644
--- a/main.py
+++ b/main.py
@@ -70,12 +70,14 @@ def gedi_bioindex(index,l1b_ds,l2a_ds, beam, beam_filt, allom_df):
beam_domain = beam_filt.loc[index]['DomainID']
try:
if pd.isnull(beam_domain):
- cval = 1.77 # 1.77 is average of all good domains alloms
+ cval = 1.63
else:
cval = allom_df[allom_df['domain']==beam_domain]['HSE'].values[0]
# get pgap
pgap = GapDS(waveform_smooth, ht_arr, np.array([rh100]), calc_refl_vg = False,
utm_x=None,utm_y=None,cval=cval)
+ # print cval to make sure all is good
+ print(cval)
except:
# bad data (fix for future)
return (np.nan,np.nan,np.nan,np.nan,np.nan)
@@ -104,7 +106,7 @@ if __name__ == '__main__':
# Read in domain polys and allom data
domain_poly_fp = os.path.join(CWD, "NEON_Domains/NEON_Domains.shp")
domain_polys = gpd.read_file(domain_poly_fp)
- allom_fp = os.path.join(CWD, "NEON-DOMAINS-HSE-edited.csv")
+ allom_fp = os.path.join(CWD, "NEON-DOMAINS-HSE-2020to2023-edited.csv")
allom_df = pd.read_csv(allom_fp)
diff --git a/notebooks/run-gedi-biomass.ipynb b/notebooks/run-gedi-biomass.ipynb
index ee11fe821650a49ddb987dcb5381c7545aa56a7a..bcc31ebab31050eae104786d3b37e8b5a0f6d737 100644
--- a/notebooks/run-gedi-biomass.ipynb
+++ b/notebooks/run-gedi-biomass.ipynb
@@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
- "execution_count": 3,
+ "execution_count": 1,
"id": "25172537-794b-4135-bb28-63c0fcefbb68",
"metadata": {},
"outputs": [
@@ -10,9 +10,9 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "WARNING:maap.maap:Unable to load config file from source maap.cfg \n",
- "WARNING:maap.maap:Unable to load config file from source ./maap.cfg \n",
- "WARNING:maap.maap:Unable to load config file from source /projects/maap.cfg \n"
+ "Unable to load config file from source maap.cfg \n",
+ "Unable to load config file from source ./maap.cfg \n",
+ "Unable to load config file from source /projects/maap.cfg \n"
]
}
],
@@ -27,15 +27,33 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 2,
"id": "f176e75b-5104-478b-ade6-a84006e966b0",
"metadata": {},
"outputs": [],
+ "source": [
+ "import time"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "f203a6c0-852b-4645-a3a5-4b65c462f4f5",
+ "metadata": {},
+ "outputs": [],
"source": []
},
{
"cell_type": "code",
- "execution_count": 2,
+ "execution_count": null,
+ "id": "b0d65f96-5dad-44e9-ae85-9d4086c4b29f",
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
"id": "b39e76ac-d765-4b8c-baf1-fe41f3296de9",
"metadata": {},
"outputs": [
@@ -43,14 +61,12 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "https://e4ftl01.cr.usgs.gov//GEDI_L1_L2/GEDI/GEDI01_B.002/2021.05.31/GEDI01_B_2021151223415_O13976_02_T00676_02_005_02_V002.h5\n",
- "\n",
- "https://e4ftl01.cr.usgs.gov//GEDI_L1_L2/GEDI/GEDI02_A.002/2021.05.31/GEDI02_A_2021151223415_O13976_02_T00676_02_003_02_V002.h5\n",
- "on file num: 1\n"
+ "on file num: 30\r"
]
}
],
"source": [
+ "# Change to appropriate filepaths for urls\n",
"l1b_urls_fpath = \"../GEDI-L1B-2021-URLS.txt\"\n",
"l2a_urls_fpath = \"../GEDI-L2A-2021-URLS.txt\"\n",
"\n",
@@ -62,7 +78,7 @@
"# Get matching string pattern and run main.py\n",
"jobs_list = []\n",
"counter=1\n",
- "for l1b_fp in l1b_fpaths:\n",
+ "for l1b_fp in l1b_fpaths[1:]:\n",
" # Get string pattern\n",
" str_pattern = re.findall(\"[0-9]{13}\", os.path.basename(l1b_fp))[0] \n",
" try:\n",
@@ -71,8 +87,8 @@
" print(\"No matching L2 file!\", l1b_fp)\n",
" continue\n",
" \n",
- " print(l1b_fp)\n",
- " print(l2a_fp)\n",
+ " # print(l1b_fp)\n",
+ " # print(l2a_fp)\n",
" job = maap.submitJob(identifier=\"single_file_test_run\",\n",
" algo_id=\"arojas_biomass_gedi\",\n",
" version=\"master\",\n",
@@ -82,15 +98,15 @@
" L2A_URL=l2a_fp)\n",
" jobs_list.append(job)\n",
" \n",
- " if counter%20:\n",
- " print(\"on file num: \", counter)\n",
- " counter+=1\n",
- " break"
+ " if counter%10==0:\n",
+ " print(\"on file num: \", counter, end='\\r')\n",
+ " time.sleep(600)\n",
+ " counter+=1"
]
},
{
"cell_type": "code",
- "execution_count": 4,
+ "execution_count": 12,
"id": "8f0b9f73-ffb1-40b7-be0e-b31480571a4a",
"metadata": {},
"outputs": [
@@ -98,17 +114,25 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "[{'job_id': 'ec2bbed4-214e-4c0b-b537-736614d43306', 'status': 'Accepted', 'machine_type': None, 'architecture': None, 'machine_memory_size': None, 'directory_size': None, 'operating_system': None, 'job_start_time': None, 'job_end_time': None, 'job_duration_seconds': None, 'cpu_usage': None, 'cache_usage': None, 'mem_usage': None, 'max_mem_usage': None, 'swap_usage': None, 'read_io_stats': None, 'write_io_stats': None, 'sync_io_stats': None, 'async_io_stats': None, 'total_io_stats': None, 'error_details': None, 'response_code': 200, 'outputs': []}]\n"
+ "WHAT\n"
]
}
],
"source": [
- "print(jobs_list[:2])"
+ "print(\"WHAT\")"
]
},
{
"cell_type": "code",
- "execution_count": 5,
+ "execution_count": null,
+ "id": "4f6093c5-1f63-4556-abb8-02714f560ad1",
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
"id": "7fe1c6f4-37c5-4fe7-b9ff-51e17b7a5cf0",
"metadata": {},
"outputs": [
@@ -117,7 +141,7 @@
"output_type": "stream",
"text": [
"Accepted\n",
- "ec2bbed4-214e-4c0b-b537-736614d43306\n"
+ "d974c84b-2691-4569-b496-1cc06380ec84\n"
]
}
],
@@ -131,10 +155,19 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 14,
"id": "2018077f-9640-4e70-bd01-a9d939b3626a",
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Succeeded\n",
+ "6152410f-1e33-4561-965a-83fd364e3767\n"
+ ]
+ }
+ ],
"source": [
"# View job status\n",
"for job in jobs_list:\n",
@@ -178,7 +211,11 @@
"id": "988420a0-1145-499c-927c-eec059c0dde9",
"metadata": {},
"outputs": [],
- "source": []
+ "source": [
+ "################\n",
+ "###############\n",
+ "##############"
+ ]
},
{
"cell_type": "code",
@@ -186,66 +223,75 @@
"id": "31626d2a-4edf-4572-81c2-7b68080e2dd3",
"metadata": {},
"outputs": [],
- "source": []
+ "source": [
+ "## Some files downloaded, other didnt (due to limit on download through USGS)"
+ ]
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 3,
"id": "9ecb7ffc-319f-40c9-8f6e-d18b6ea1c890",
"metadata": {},
"outputs": [],
- "source": []
+ "source": [
+ "import glob\n",
+ "indir = \"/projects/my-private-bucket/dps_output/arojas_biomass_gedi\"\n",
+ "csv_list = []\n",
+ "for subdir, dirs, files in os.walk(indir):\n",
+ " for file in files:\n",
+ " if file.endswith(\".csv\"):\n",
+ " # fp = os.path.join(subdir, file)\n",
+ " # print(fp)\n",
+ " # csv_list.append(fp)\n",
+ " csv_list.append(file)\n",
+ " "
+ ]
},
{
"cell_type": "code",
- "execution_count": 1,
- "id": "77a995d1",
+ "execution_count": 4,
+ "id": "f3ae4e2c-fa90-41ae-8fa2-9e3fd1241157",
"metadata": {},
"outputs": [
{
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "WARNING:maap.maap:Unable to load config file from source maap.cfg \n",
- "WARNING:maap.maap:Unable to load config file from source ./maap.cfg \n",
- "WARNING:maap.maap:Unable to load config file from source /projects/maap.cfg \n"
- ]
+ "data": {
+ "text/plain": [
+ "524"
+ ]
+ },
+ "execution_count": 4,
+ "metadata": {},
+ "output_type": "execute_result"
}
],
"source": [
- "import os\n",
- "import re\n",
- "from maap.maap import MAAP\n",
- "import re\n",
- "# maap = MAAP(maap_host='api.maap-project.org')\n",
- "maap = MAAP(maap_host='api.maap-project.org')"
+ "len(csv_list)"
]
},
{
"cell_type": "code",
- "execution_count": null,
- "id": "bb5b4efc",
- "metadata": {},
- "outputs": [],
- "source": []
- },
- {
- "cell_type": "code",
- "execution_count": 3,
- "id": "e598e092",
+ "execution_count": 5,
+ "id": "5bb204a4-e7d4-4a83-898f-81db03d080aa",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
- "https://e4ftl01.cr.usgs.gov//GEDI_L1_L2/GEDI/GEDI01_B.002/2021.05.31/GEDI01_B_2021151223415_O13976_02_T00676_02_005_02_V002.h5\n",
- "\n",
- "https://e4ftl01.cr.usgs.gov//GEDI_L1_L2/GEDI/GEDI02_A.002/2021.05.31/GEDI02_A_2021151223415_O13976_02_T00676_02_003_02_V002.h5\n",
- "on file num: 1\n"
+ "done\n"
]
}
],
+ "source": [
+ "print(\"done\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 6,
+ "id": "bb5b4efc",
+ "metadata": {},
+ "outputs": [],
"source": [
"l1b_urls_fpath = \"../GEDI-L1B-2021-URLS.txt\"\n",
"l2a_urls_fpath = \"../GEDI-L2A-2021-URLS.txt\"\n",
@@ -266,107 +312,27 @@
" except:\n",
" print(\"No matching L2 file!\", l1b_fp)\n",
" continue\n",
- " \n",
- " print(l1b_fp)\n",
- " print(l2a_fp)\n",
+ " \n",
+ " # Check if file was already downloaded\n",
+ " date_str = os.path.basename(l1b_fp).split(\"_\")[2]\n",
+ " if any(date_str in x for x in csv_list):\n",
+ " continue\n",
+ " \n",
+ " # print(l1b_fp)\n",
+ " # print(l2a_fp)\n",
" job = maap.submitJob(identifier=\"single_file_test_run\",\n",
- " algo_id=\"arojas_biomass_gedi_conus\",\n",
+ " algo_id=\"arojas_biomass_gedi\",\n",
" version=\"master\",\n",
" username=\"arojearthdata\",\n",
- " queue=\"maap-dps-worker-8gb\",\n",
+ " queue=\"maap-dps-worker-16gb\",\n",
" L1B_URL=l1b_fp,\n",
" L2A_URL=l2a_fp)\n",
" jobs_list.append(job)\n",
" \n",
- " if counter%20:\n",
- " print(\"on file num: \", counter)\n",
- " counter+=1\n",
- " break"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 4,
- "id": "273c2151",
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "[{'job_id': 'e02adfbd-c1f1-417f-9563-d158eafed27c', 'status': 'Accepted', 'machine_type': None, 'architecture': None, 'machine_memory_size': None, 'directory_size': None, 'operating_system': None, 'job_start_time': None, 'job_end_time': None, 'job_duration_seconds': None, 'cpu_usage': None, 'cache_usage': None, 'mem_usage': None, 'max_mem_usage': None, 'swap_usage': None, 'read_io_stats': None, 'write_io_stats': None, 'sync_io_stats': None, 'async_io_stats': None, 'total_io_stats': None, 'error_details': None, 'response_code': 200, 'outputs': []}]\n"
- ]
- }
- ],
- "source": [
- "print(jobs_list[:2])"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 5,
- "id": "27f8a6cd",
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Accepted\n",
- "e02adfbd-c1f1-417f-9563-d158eafed27c\n"
- ]
- }
- ],
- "source": [
- "# View job status\n",
- "for job in jobs_list:\n",
- " print(job.retrieve_status())\n",
- " print(job.id)\n",
- " break"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 19,
- "id": "758ab8f6",
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Running\n",
- "e02adfbd-c1f1-417f-9563-d158eafed27c\n"
- ]
- }
- ],
- "source": [
- "# View job status\n",
- "for job in jobs_list:\n",
- " print(job.retrieve_status())\n",
- " print(job.id)\n",
- " break"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 6,
- "id": "dcfc811e",
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "['http://maap-ops-workspace.s3-website-us-west-2.amazonaws.com/dataset/triaged_job/arojas_biomass_gedi_conus/master/2023/09/27/4ad5a4ee-4859-47aa-b825-d2a85562129c', 's3://s3-us-west-2.amazonaws.com:80/maap-ops-workspace/dataset/triaged_job/arojas_biomass_gedi_conus/master/2023/09/27/4ad5a4ee-4859-47aa-b825-d2a85562129c', 'https://s3.console.aws.amazon.com/s3/buckets/maap-ops-workspace/dataset/triaged_job/arojas_biomass_gedi_conus/master/2023/09/27/4ad5a4ee-4859-47aa-b825-d2a85562129c/?region=us-east-1&tab=overview', '+ export HOME=/root\\n+ HOME=/root\\n+ exec /docker-stats-on-exit-shim _docker_stats.json /app/dps_wrapper.sh /app/biomass-gedi-conus/run.sh \\'https://e4ftl01.cr.usgs.gov//GEDI_L1_L2/GEDI/GEDI01_B.002/2021.05.31/GEDI01_B_2021151223415_O13976_02_T00676_02_005_02_V002.h5\\n\\' https://e4ftl01.cr.usgs.gov//GEDI_L1_L2/GEDI/GEDI02_A.002/2021.05.31/GEDI02_A_2021151223415_O13976_02_T00676_02_003_02_V002.h5\\n+ /app/biomass-gedi-conus/run.sh \\'https://e4ftl01.cr.usgs.gov//GEDI_L1_L2/GEDI/GEDI01_B.002/2021.05.31/GEDI01_B_2021151223415_O13976_02_T00676_02_005_02_V002.h5\\n\\' https://e4ftl01.cr.usgs.gov//GEDI_L1_L2/GEDI/GEDI02_A.002/2021.05.31/GEDI02_A_2021151223415_O13976_02_T00676_02_003_02_V002.h5\\nMatplotlib created a temporary cache directory at /tmp/matplotlib-u_3gfo0a because the default path (/root/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.\\nFontconfig error: No writable cache directories\\nTraceback (most recent call last):\\n File \"fiona/ogrext.pyx\", line 136, in fiona.ogrext.gdal_open_vector\\n File \"fiona/_err.pyx\", line 291, in fiona._err.exc_wrap_pointer\\nfiona._err.CPLE_OpenFailedError: /data/work/jobs/2023/09/27/05/17/job-arojas_biomass_gedi_conus__master-20230927T051209.837755Z/NEON_Domains/NEON_Domains.shp: No such file or directory\\n\\nDuring handling of the above exception, another exception occurred:\\n\\nTraceback (most recent call last):\\n File \"/app/biomass-gedi-conus/main.py\", line 108, in <module>\\n domain_polys = gpd.read_file(domain_poly_fp)\\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\\n File \"/opt/conda/envs/osgeo-env/lib/python3.11/site-packages/geopandas/io/file.py\", line 281, in _read_file\\n return _read_file_fiona(\\n ^^^^^^^^^^^^^^^^^\\n File \"/opt/conda/envs/osgeo-env/lib/python3.11/site-packages/geopandas/io/file.py\", line 322, in _read_file_fiona\\n with reader(path_or_bytes, **kwargs) as features:\\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\\n File \"/opt/conda/envs/osgeo-env/lib/python3.11/site-packages/fiona/env.py\", line 457, in wrapper\\n return f(*args, **kwds)\\n ^^^^^^^^^^^^^^^^\\n File \"/opt/conda/envs/osgeo-env/lib/python3.11/site-packages/fiona/__init__.py\", line 292, in open\\n colxn = Collection(\\n ^^^^^^^^^^^\\n File \"/opt/conda/envs/osgeo-env/lib/python3.11/site-packages/fiona/collection.py\", line 243, in __init__\\n self.session.start(self, **kwargs)\\n File \"fiona/ogrext.pyx\", line 588, in fiona.ogrext.Session.start\\n File \"fiona/ogrext.pyx\", line 143, in fiona.ogrext.gdal_open_vector\\nfiona.errors.DriverError: /data/work/jobs/2023/09/27/05/17/job-arojas_biomass_gedi_conus__master-20230927T051209.837755Z/NEON_Domains/NEON_Domains.shp: No such file or directory\\n+ cp _stderr.txt _alt_traceback.txt\\n']\n"
- ]
- }
- ],
- "source": [
- "# Retrieve results\n",
- "for job in jobs_list:\n",
- " print(job.retrieve_result())\n",
- " break"
+ " if counter%10==0:\n",
+ " print(\"on file num: \", counter, end='\\r')\n",
+ " time.sleep(600)\n",
+ " counter+=1"
]
},
{